► Glycans play roles in many biological process and are involved in all major diseases. ► Population studies revealed high variability in glycome composition. ► Genomics, epigenomics, glycomics and other omics need to be combined. ► First studies integrating glycomics, genomics and epigenetics have been published. Majority of eukaryotic proteins are glycosylated and their glycan moieties have numerous important structural, functional and regulatory roles. Because of structural complexity of glycans and technological limitations glycomics, and particularly glycoproteomics was not able to follow rapid progress in genomics and proteomics over last 30 years. However, the field of glycan has been progressing rapidly and first large-scale studies of the glycome have been completed recently. These studies have revealed significant differences in glycome composition between individuals, which may contribute to the human phenotypic variability. The current state-of-the-art in high-throughput glycomics and its integration with genomics, epigenomics and lipidomics is reviewed in this article.